In the final installment of this season of Titans of Science, Chris Smith speaks with Sharon Peacock, one of the UK’s leading voices in infectious disease research. She is best known for her work on whole genome sequencing of pathogens such as MRSA and SARS CoV-2, and studies of antimicrobial resistance...
In this episode
01:34 - Sharon Peacock: Dentistry to infectious diseases
Sharon Peacock: Dentistry to infectious diseases
Sharon Peacock was born in Ramsgate in Kent on the 24th of March 1959. She attended Harlands Primary School in Haywards Heath and then Warden Park School in Cuckfield. She left school at 16 to train initially as a dental nurse and then as a general adult nurse. She specialised in end-of-life care but then pivoted to study medicine in her mid-20s at the University of Southampton. She sat on the board of Cambridge University Hospitals for almost a decade and she's also served as the founding director of the COVID-19 Genomics UK consortium that was set up during the pandemic. Over three decades Sharon has become one of the UK's leading voices in infectious diseases research. She's best known for her work on whole genome sequencing of pathogens, antimicrobial resistance and diseases like melioidosis and MRSA. Sharon's contributions have included 600 scientific papers and major leadership roles in national public health initiatives. She was appointed Master of Churchill College in 2024. I'm pleased to say she's joining me now at your rivals at Queens' College, Sharon. Good to see you, actually in the flesh because we spent a lot of time together almost every day during COVID in electronic means didn't we?!
Sharon - Yes, it's been a joyful ride actually through healthcare and science. So I had no direction when I was at school at all. I left at 16. I didn't know where my career would take me. I just left school and worked in a shop, but in that street was a dental surgery and they advertised in our shop with a little sort of post-it note saying "Apply to become a dental nurse", and so I walked up the street. I applied to become a dental nurse, and in many ways, that was my gateway. So I walked through that gateway. I think at that time when I was young, it did a couple of things. First of all, it taught me that I really enjoyed healthcare, and I think the other thing it taught me is the value of work. I suddenly found, having probably been a bit of a slouch at school, that I loved working. I loved working really hard. I ran the whole practice — a single-handed practice — but I really enjoyed it, and it made me feel that I had a purpose in my life.
Chris - But you didn't have any A-levels. So how did you manage to get to university to study medicine?
Sharon - I did it through a transition through nursing. So when I was a dental nurse, I really enjoyed it. I used to go a day a week — or an evening a week, actually — to Brighton to do the theory behind dental nursing and teeth. And actually, I took the step. I moved to Brighton full-time and trained as a general adult nurse, and it was really six months in that I thought, this is fascinating. The body is fascinating. I really liked learning about how it goes wrong, why it goes wrong, how you can help people with their health, with treatments and so on. Six months in, standing on this male medical ward, thinking — it was like a light bulb moment — I want to be a doctor. But I didn't dare tell anyone. I didn't have enough qualifications. So I finished my nursing training and, as soon as I could, I went back to night school to get my GCSEs, then to technical college part-time to get my A-levels, and that is where the table was really lit around science. So I was really interested in the body, but then I got the chance to study A-levels and that was tremendous fun, actually.
Chris - Why didn't you do that initially? You said you were a bit of a slouch at school. Was it just that your fire had not been lit? Were you a late bloomer? Was there something about it that was a bit unexhilarating at the time, and it took the insight of actually being there in that place, thinking "I could do that", that then got you going?
Sharon - I didn't think I was very smart, and I don't think anyone at my school thought I was very smart, and so I was not encouraged to do the GCSEs. I thought, well, I don't have the ability to do it. And so it's so much about environment. If people say, you know, "It's really great, go for it, this is really interesting, this is why you should be really fired up about that" — that environment's really important to your learning. But if you haven't got that, and my parents were not academic, and none of my extended family are academic, I didn't see the point.
Chris - You go to Southampton University, you turn into a doctor, but then presumably that itch comes back again because then you think, "I think I'm going to be a scientist now."
Sharon - Well, I don't think the itch ever left — I mean, it's a constant itch. So I went to Southampton, completely in my element. I unfurled my academic wings. Nobody could tell me not to go to the library till 10, and I just loved to learn — I really loved it. Once I'd qualified as a doctor, I spent quite a few years in general internal medicine, so I did all the relevant exams. I was doing cardiology, respiratory medicine, running the cardiac arrest team — I loved all that. And I saw myself being a practising doctor for the rest of my career. But then I got a job in Oxford as a kind of middle-grade doctor, and I was fortunate to go and work on an infectious diseases ward and also interact with people who were really interested in microbiology. And it was there that I decided I liked that specialty. But also, it was there that it was really quite the norm to consider doing a PhD. So I did a PhD really because I thought it was very interesting to dive even deeper into a subject. And then the rest is history — I combined medicine with being a scientist.
Chris - That gets you into infectious diseases, which has been the thrust of what you've done ever since. But your mega contribution has been reading the genetic code of these bugs. So how did that start to happen? Because at the time when you would have been getting into all of this, the Human Genome Project was ticking along — it hadn't reported yet, it was just beginning to get going. You had John Sulston down at the Sanger, beginning to develop ways to read genetic codes much faster. I mean, previously people were struggling to read a handful of genetic base pairs a week, weren't they? So how did you bring that to bear on the infectious diseases problem?
Sharon - Well, I was working in Southeast Asia actually, in Thailand. I went there in 2003 and I was studying tropical infectious diseases, and I had the opportunity to work with the Wellcome Sanger Institute to select some isolates for whole genome sequencing, which was revolutionary at the time. I then created a link and started to understand what whole genome sequencing could really tell you about a pathogen — very deep information about its structure and function from the genome perspective. And in 2009, my family and I came back from Thailand, and I thought, well, this is a moment in time when the technology is really changing for sequencing. So when I was involved in those earlier years in sequencing, you had to do it in a very specialist institution like the Sanger Institute — you couldn't do it yourself. But there was a moment in time when that was all about to change. You could actually purchase things that looked like a cappuccino machine, to sequence pathogens. In fact, you could even have handheld sequencers. And so I saw that moment as a transitionary period where I thought, well, what could I do if I had access to that right in the clinical laboratory, by hospital patients? What could I do with that? And that's what really got me fired up, and that's where I really started to experiment with what questions I could ask of that genome information and how that could help patients and public health.
09:22 - Sharon Peacock: Saving lives through sequencing pathogens
Sharon Peacock: Saving lives through sequencing pathogens
Sharon Peacock describes her pioneering work sequencing the genomes of pathogens in hospital environments to detect dangerous bugs...
Sharon - In some ways I wasn't certain, but there are a couple of areas which I thought we could really improve on. The first was that when you think about an outbreak of an infectious disease, it’s best-guess work. You're looking at how people might have shared a time in a space to see whether a pathogen has passed from one person to another. Or looking at, for example, a foodborne outbreak where everyone’s eaten the same contaminated dish with salmonella or whatever — it's what I would call shoe-leather epidemiology. It's what John Snow did with cholera. So you're thinking about how it fits together by people being in contact with each other or having a point source, like contaminated food. But I thought — what if you could sequence the pathogens from different people, compare the full length of that genome, and see whether they’re very related — which means that it’s likely to have been an outbreak — or very unrelated, in which case it’s pure chance? So that was the first area I wanted to test, and I wanted to test that in hospitals where we had outbreaks of this pathogen, MRSA — methicillin-resistant Staphylococcus aureus — to see whether we were much better using sequencing than we had been with this shoe-leather epidemiology.
The second area I was really curious about was whether we could use sequencing to work out if a given pathogen was susceptible or resistant to a certain antibiotic. So, for example, in tuberculosis, it can take weeks or months to work that out in the laboratory. What if you could actually sequence — how quickly could you get an answer by looking at the genes that code for resistance and therefore speed up treatment? So those are the two areas that I was particularly interested in.
Chris - What was the first kind of detective story that you went for with this to prove this could bear fruit?
Sharon - The first one was really around MRSA. So this is a bacterium that can cause outbreaks in hospitals, and it comes back to: do you have an outbreak — in which case you really need to dive in and do some interventions to bring it to a close — or do a cluster of patients actually have MRSA and they’re together quite by chance, in which case it's less of a worry? There was a cluster of babies on a neonatal intensive care unit at our hospital and it looked as if there might be an outbreak going on there. In fact, this was stuttering on for about six months, but there were lots of signs that it wasn’t an outbreak based on the way people usually look at this — in terms of time and space — you know, big gaps between some babies and then the next group coming along who had MRSA. So what I did was actually sequence those MRSA that were stored in the freezer, and I looked at whether there was an outbreak — and indeed, they were all related. Those bugs were all related. So there was definitely an outbreak over six months.
Chris - Your argument being, if they’re all genetically identical to each other, one must have got it from the other — that’s why they’re genetically the same. The chance of that happening by chance is so remote, it just wouldn’t happen.
Sharon - Exactly right. So they were very, very closely related. If this wasn’t an outbreak, you’d expect them to be quite unrelated — their genetic code would be different. So we said, well, this is better than current practice. But we then went one step further — we went to the laboratory where MRSA is isolated from samples sent in from GPs, and we sequenced a whole bunch of these MRSA isolates. And there were some matches to this outbreak in the neonatal intensive care unit. And we were scratching our heads thinking, how can that be?
Actually, when we delved into their medical records, what we found was that there were parents of these infants and people who’d been in contact with these infants who had acquired carriage of this organism — because you often carry it harmlessly — but they developed infections. So not only were we better than standard practice at defining an outbreak, but the reach we had into the community was much bigger. Those cases would not have been detected before. So that was, I guess, forensic genomic epidemiology — trying to work out who's involved in an outbreak.
Chris - That presumably means you can then improve approaches in the hospital. Because if you can show there's been a chain of transmission, you can then ask, well, why did that person give it to that person? Did it go via the staff? What do I have to do to block that in future?
Sharon - Yeah, I mean, the whole point of doing this is to make our practice safer. If people have got a feedback loop — “Yes, you did have an outbreak” or “Actually, no, we've excluded it” — that can help them to improve their practice. For example, handwashing or cleanliness and so on — there are lots of things you can do to reduce the transmission of these organisms, which tend to be carried on hands by healthcare workers from one patient to another.
But actually, if we could sequence the first two or three examples of, say, MRSA that were coming through the hospital and find that they are related, we can detect an outbreak much quicker than if we wait for two weeks and just watch and wait to see if any more cases come along. You're not quite sure if there’s an outbreak or not. Instead, it’s like: you sequence first, you look at the link in time and space, and that is a much more accurate way of working out if you have an outbreak. So not only could you improve practice after you’ve decided there’s an outbreak — you could detect the outbreak much quicker and prevent other cases from getting involved.
Chris - What was the reaction like once you showed you could do this and do it meaningfully? How did people react?
Sharon - I would respond in a couple of ways. First of all, it was an explosive finding — very, very exciting. Lots of people got incredibly excited that this was a possibility. In many ways, it was no great surprise that it worked — if you know about genome sequencing, you might predict it would work — but it was really a very important finding for the scientific community.
Hospitals were also really excited about it. But one of the things that I feel we need to do more on is getting this into routine care. We know it helps. We know it detects outbreaks quicker and more accurately. So my initial response was: great, we can get this rolled out into the hospital for all sorts of things — MRSA and multi-drug resistant gram-negative organisms, the sorts of things that circulate in hospitals. But it’s proved to be quite challenging to do that.
Chris - Why?
Sharon - Well, I think there’s a range of reasons. First of all, you need the equipment. You need the money to be able to do it, because this isn’t a diagnostic test — it’s for public health and outbreak analysis. So you have to think about how you’re going to fund it. You need to train the people to do it. You need to standardise the methodology. And you also need to be able to interpret the genome data, which needs automated systems. And I would say one of the biggest stumbling blocks is that — having an automated system where you don’t need an expert to read that genome sequence and compare it with another isolate — that’s one of the biggest stumbling blocks. You want the kind of information-in, answer-out system: Yes, there’s an outbreak or No, there’s not an outbreak. What you can’t have is a bank of bioinformaticians sitting there tapping away at the keyboard looking at the genome data itself. It has to be quick — and we don’t have that at the moment.
Chris - What about the answer to: Is this TB isolate resistant to this antibiotic? — the other important question, because that’s a massive issue, especially now with rising antimicrobial resistance?
Sharon - Well, that’s also been a huge success story — and by the work of a great many people. So sequencing of parts of the TB genome can indeed predict if an organism is going to be susceptible or resistant to the treatment that you want to give. And that’s incredibly important when you think about multi-drug resistant or extremely drug-resistant TB, where it can take many months to get that answer. Actually, the UK was one of the first countries to bring that in as a routine — so TB isolates are all sequenced now, which can guide treatment. I think there was some scepticism about whether that was going to be an effective technique, but actually, worldwide now, it’s realised that that is the way to go — with TB sequencing to predict treatment.
18:21 - Sharon Peacock: Catching changes in the COVID virus
Sharon Peacock: Catching changes in the COVID virus
Sharon Peacock explains how effective genome sequencing can be for helping health professionals better understand viruses, which became very important a few years ago...
Sharon - I would say that before the pandemic, one virus that is very important to sequence is HIV. People who are treated with what's called antiretroviral therapy, which suppresses the virus in the body, can develop resistance to the treatment. What you really need to do is sequence parts of the virus to see whether the treatment you're going to give is effective or not. You can't do that in a test tube. You need to be able to sequence it. So sequencing has actually been really important for HIV treatment.
Chris - So you prove all this, and that was looking like a huge success story, and then a pandemic comes. And this is when really you took the knowledge that you'd gained and kind of gave it the biggest dose of steroids it ever could because all of a sudden you're in charge of what became the COVID Genomics Consortium for the UK. The whole world was looking at that data. Why don't you just outline for us exactly, a) what you did, and b) what it produced?
Sharon - When the pandemic began, it was clear that we would need to start sequencing the virus to look for changes in its genome. Changes in the genome could, for example, relate to changes in how it behaves — changes in transmissibility or the way it interacts with our immune system, for example — which could affect vaccine efficacy and the way it causes disease in people. Would it cause a more severe disease, or a less severe one? I considered it very likely that we'd need to sequence the virus. So myself and Patrick Vallance, the Chief Scientific Adviser to the UK at the time, had discussions and agreed that I would set up a sequencing capability for the UK.
Chris - That was very early then. Was this literally at the beginning of the pandemic? You said, look, we've got a problem. This is one way we should be addressing it.
Sharon - Yes, absolutely. It was before we had barely any cases in the UK, but we needed to prepare. It wasn't going to be something we could get ready overnight. It was going to be a massive enterprise to set this up. So the point of sequencing the virus was really to detect if it mutated or changed its sequence, which could lead to changes in how it was transmitted from one person to another, the rate at which that happened, or how it interacted with our immune system. That would relate to vaccine efficacy or the severity of the disease people developed. We needed a countrywide view.
So we aimed to set up a sequencing capability across the United Kingdom. We pulled together the four public health agencies of the UK, 16 academic universities and the Wellcome Sanger Institute. We connected that like a network to 100 NHS testing labs, and as they developed, all of the Lighthouse Labs doing community testing. If there was a positive sample, we would obtain it, sequence the virus, and look at its genome to see how it was evolving.
Chris - And so when people were seeing reports of what variant is prominent at the moment, that was your data that was informing what's on this almost virological radar screen for the country, really.
Sharon - Exactly. We aimed to sequence around 10% of all known positive cases. We generated all of the data. We put all the genome data into a secure database that could be accessed by scientists. It could also be accessed by public health agencies, so they could monitor what was happening in their regions. We also, in an anonymous way, deposited all of those genomes into an international database. People could see what was happening in our country from a genome perspective. We had open-source information, which was very helpful, given that this was a global pandemic.
Chris - Britain was effectively then a sort of barometer for the evolution of the virus. Did other countries then either want to work with you, or did they set up an equivalent taking a lead from what you were doing, to add to that and turn it into a global radar screen?
Sharon - Yes. Other countries were thinking about this too. At one point, nearly half of the genomes deposited into the international database were generated in the UK. We were one of the first out of the starting blocks to generate this kind of information. Others were hot on our heels — for example, South Africa was very effective, as were the Netherlands and Denmark.
I think the great pity for me was that many countries didn't have the resources to sequence, so they weren't in a position to understand what was circulating. And it also meant that when a new variant emerged — and it could emerge anywhere — we wouldn’t detect it quickly. Alpha emerged in Kent, but other variants emerged elsewhere. To detect them, we needed a global effort, and that came quite late.
Chris - Those data all exist now, don’t they? So presumably there are people mining into that, delving into it to learn things, even though the pandemic is thankfully in the past. The way you did that stands there as an example of how it can be done. And it's an enormous resource for us to continue to learn from.
Sharon - Yes. What it showed for the first time was that sequencing could be done on a very large scale. That was unheard of. You could sequence millions of viral genomes and make sense of that in terms of the virus’s evolution and what it means for us as humans. That was a moment in time when sequencing pathogens really came onto most people's radar, and they realised the true power of doing it. There were other lessons too from how we set it up. One of them was to go into action without hesitation. People might have thought, “You're wasting your time setting that up now,” but you can't move fast enough in a pandemic. The speed and the confidence with which we said, “This will be important,” mattered. The worst outcome would have been ending up with a lot of valuable scientific data — which is no bad thing. But the best outcome was the one we had: we could track the emergence of variants and understand what that meant for humans.
Chris - Is this policy for a future pandemic or Disease X now? Will they be back on the phone to you? Is it written in, baked in, that when the next pandemic lands, they’ll call Sharon to do this again?
Sharon - It's not baked in that they would call me. The COG-UK Consortium was closed down after three years. It had 600 people, mostly volunteers. They were paid by their universities or employers, but volunteered for us. What I would say is that if another pandemic comes along, we absolutely need to be sequencing that virus or organism as soon as possible and doing the same. We have created a blueprint for how you can do this, but COG-UK as an entity is no longer in existence. Public health agencies will have the capability to do sequencing on a smaller scale, but we've learned invaluable lessons from that process.
Chris - Some would say, though, that if we wait for the next pandemic, we've waited too long. Shouldn't we be doing this anyway, right now?
Sharon - There is a lower amount of sequencing, but in virological peacetime, public health agencies have other priorities. They'll use sequencing for TB, outbreaks, foodborne outbreaks, and so on. So the capabilities are there. I’d just say that the scale is not there for a global pandemic — that would need to be scaled up quickly.
Chris - People really noticed though, didn’t they? When the consortium stopped, it was almost like that radar screen went dark. You heard reporters, health commentators, and other medics saying, “We don’t know what variants are out there now. We don’t know what will be going into the vaccine because we can't get that sense of the trend of what the virus is doing,” that we had when it was active. It really was incredibly meaningful and very useful.
Sharon - I can only agree.
27:19 - Sharon Peacock: Running a Cambridge college
Sharon Peacock: Running a Cambridge college
Sharon Peacock on her current role at Churchill College, Cambridge...
Sharon - It wasn't like that at all. I see this as coming full circle, actually. I left school at 16. I wish I'd had the opportunity to go to university at 18. I'm passionate about outreach for Cambridge colleges. They are places that are for the academically able— and that's the only barrier. If you're academically able, come to Cambridge. So going to a college is like coming full circle: really supporting young people to apply, to support them to do well in their exams, but also in their welfare. And I love the energy that young people have, actually. To see them thriving at Cambridge, in Churchill College, it's the best job in the world.
So much of what I do is relatively mundane; I chair lots of committees, I help the college make good decisions. But I really relish seeing our students do well and go out into the world and bring that energy, enthusiasm, and knowledge to make it a better place. I also work very hard to ensure that the college will still be standing in 50 or 100 years. We're doing a lot of planning— improving our infrastructure, improving our buildings, improving our endowment, our money— so we can continue to make that offer to young people in perpetuity.
Chris - Is there still time for science, though? Because this is a pretty big job.
Sharon - There's still time for lots of things, actually. I'm a very energetic person, I guess. And I do many other things. I still have a contract with the Clinical School. I still do research. And I do other things. I'm a trustee on various charities, and so on, as well as balancing that with fitness, running, and so on. I like to fill my day and make it really interesting. And that's going to be a lifelong habit, I think. I can't break that habit.
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